Epigenetic T Cell Reprogramming for ACT Persistence
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Solution Overview
Problem
Current Adoptive Cell Therapy (ACT) treatments for diseases like cancer face challenges such as suboptimal T cell function, expansion, and persistence, necessitating new methods to enhance T cell phenotype and activity.
Innovation Solution
An epigenetic-modifying DNA-targeting system comprising a DNA-targeting domain capable of targeting specific sites in T cells and an effector domain that increases transcription, promoting a stem cell-like memory T (TSCM) cell phenotype without introducing genetic disruptions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If current ACT treatments are used, then T cell therapy can be administered, but T cell function, expansion, and persistence remain suboptimal
Solution Approach 1:
The patent changes the epigenetic parameters of T cells by using CRISPR-dCas9 epigenetic editing systems to modify histone modifications and DNA methylation patterns at specific gene loci. This epigenetic reprogramming transforms T cell phenotype from exhausted or memory-differentiated states back to a stem cell-like memory state, thereby improving both reliability of T cell function and productivity of T cell expansion and persistence
Solution Approach 2:
The patent applies epigenetic editing in advance to reprogram T cells before they are administered to the patient. By pre-modifying the epigenetic landscape of T cells to express stem cell-like markers (CD45RA+, CCR7+, CD27+) and exhaustion-inhibiting genes (TOX, NR4A1, PD-1), the T cells are prepared beforehand to ensure optimal function, expansion, and persistence upon administration, rather than attempting to correct these issues after T cell exhaustion occurs in vivo
2Duration of action of stationary object
If epigenetic editing is used to promote TSCM phenotype, then T cell persistence and expansion improve, but system complexity increases
Solution Approach 1:
The patent segments the epigenetic editing system into modular components: (1) CRISPR-dCas9 fusion protein with specific effector domains for epigenetic modification, (2) guide RNAs targeting specific gene loci, and (3) separate delivery vectors for each component. This segmentation allows for standardized, interchangeable modules that can be recombined for different T cell reprogramming goals, thereby managing complexity while achieving durable T cell persistence through epigenetic reprogramming
Solution Approach 2:
The patent uses intermediary molecules to bridge the complexity of epigenetic editing with the simplicity of T cell therapy. Specifically, CRISPR-dCas9 fusion proteins act as intermediaries that deliver epigenetic modifications without causing DNA breaks, and guide RNAs serve as intermediaries that direct these modifications to specific gene loci. These intermediaries enable precise epigenetic control to promote TSCM phenotype and long-term persistence while maintaining system manageability through RNA-mediated targeting
3Manufacturing precision
If transcription activation is used to promote TSCM phenotype, then T cell phenotype improves, but risk of genetic disruption increases
Solution Approach 1:
Instead of using traditional CRISPR-Cas9 nuclease that cuts DNA to activate genes (which carries risk of off-target mutations and genetic disruption), the patent inverts the approach by using catalytically dead dCas9 that cannot cut DNA. The activation is achieved through epigenetic modification (histone acetylation, methylation) and recruitment of transcriptional co-activators to gene promoters, thereby achieving precise T cell phenotype control while eliminating the harmful effect of DNA cleavage and genetic disruption
Solution Approach 2:
The patent substitutes the mechanical DNA-cutting mechanism of CRISPR-Cas9 nuclease with an epigenetic modification mechanism using dCas9 fused to epigenetic effectors (HDACs, HATs, methyltransferases). This replacement eliminates the need for physical DNA breakage and repair, thereby achieving precise transcriptional activation for TSCM phenotype control without the harmful effects of genomic DNA disruption, off-target mutations, or chromosomal rearrangements
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The system effectively enhances T cell persistence, expansion, and anti-tumor activity by promoting a TSCM cell phenotype, characterized by specific cell-surface markers and polyfunctional activity, thereby improving the efficacy of ACT.
Implementation Method 1
The provided epigenetic modifying DNA-targeting systems of the present disclosure bind to or target a target site in a gene or regulatory element thereof in a T cell
Implementation Method 2
at least one effector domain capable of increasing transcription of the gene; wherein increased transcription of the gene promotes a stem cell-like memory T (TSCM) cell-like phenotype
Data Source
AI summary
Provided in some aspects are epigenetic-modifying DNA-targeting systems, such as CRISPR-Cas/guide RNA systems, that bind to or target a target site in a gene or regulatory element thereof in a T cell. In some aspects, the provided epigenetic modifying DNA-targeting systems provided herein modulate a T cell phenotype or activity. In particular, the provided embodiments relate to the transcriptional activation of genes that promote a stem cell-like memory T (TSCM) cell phenotype. In some aspects, also provided are compositions, polynucleotides, vectors, cells, and pluralities and combinations thereof, and methods and uses related to the provided epigenetic-modifying DNA-targeting systems, for example in modulating the phenotype in T cells including in connection with adoptive T cell therapy.